[gmx-users] Methodology Check

Tom Dupree t.dupree at unsw.edu.au
Wed Apr 6 07:54:19 CEST 2011

Greetings all,

I am trying to learn/use GROMACS for evaluating ligand dockings.

After some effort I managed to get a run through EM, equilibration and production with protein and water.

I am now having some difficulty getting a similar run going with a ligand.

I am not ready to talk about the specific problems I am having but I was wondering if someone could check my approach/methodology is correct and if I am doing something GROMACS doesn't like/fundamentally wrong.

I have an .itp from the ATB.
I take my .pdb and remove the ligand.
I run PDB2GMX on the no_lig.pdb and get a .top and a new no_lig2.pdb
I edit the .top
and add #include "lig.itp"
I use editconf on the no_lig2.pdb -bt cubic -d 0.5
I use genbox to insert the lig.pdb into the no_lig2.pdb and get complex.pdb
I use genbox to solvate complex.pdb and return complex.gro as well as an updated .top
I use grompp to process my em.mdp .top and complex.gro and get complex.tpr       <- (my current problem step)
I use mdrun complex.tpr and get my trajectory
repeat last two steps for equilibration and production.

I have not used genion yet, I assumed that it would affect the simulation accuracy but not its ability to run, I am currently +13.
I also realise that I do not have position restraint files for the ligand at the moment so equilibration wont be correct. 

all the best,


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